R: Read an OCG Partition File into R

read.OCG {linkcomm} | R Documentation

## Read an OCG Partition File into R

### Description

This function reads in an OCG partition file and converts it into an OCG object for use in R.

### Usage

    read.OCG(file, elfile = NULL, verbose = FALSE, keep.out = FALSE)

### Arguments

`file` | A character string naming the OCG partition file.
`elfile` | A character string naming the file containing the network that the OCG partition is based upon.
`verbose` | Logical, whether to print progress to the screen. Defaults to FALSE.
`keep.out` | Logical, whether to keep the intermediate files written when reading in the OCG partition. Defaults to FALSE.

### Value

An object of class `OCG`, which is a list containing the following elements:

`numbers` | An integer vector with the number of edges, nodes, and communities.
`modularity` | An integer number specifying the modularity of the network.
`Q` | A real number specifying the value of Q generated by the OCG algorithm.
`nodeclusters` | A data frame consisting of 2 columns; the first contains node names, and the second contains single community IDs for each node. All communities and their nodes are represented, but not necessarily all nodes.
`numclusters` | A named integer vector. Names are node names and integer values are the number of communities to which each node belongs.
`igraph` | An object of class `igraph`. The network is represented here as an `igraph` object.
`edgelist` | A character matrix with 2 columns containing the nodes that interact with each other.
`clustsizes` | A named integer vector. Names are community IDs and integer values indicate the number of nodes that belong in each community.

### Author(s)

Alex T. Kalinka alex.t.kalinka@gmail.com

### References

Kalinka, A.T. and Tomancak, P. (2011). linkcomm: an R package for the generation, visualization, and analysis of link communities in networks of arbitrary size and type. Bioinformatics 27, 2011-2012.

### Examples

    ## Read an OCG partition file into R.
    ## Not run: oc <- read.OCG(file = "OCG_partition.txt", elfile = "network.txt")

[Package linkcomm version 1.0-14 Index]